SNPs in a Large Genomic Scaffold Are Strongly Associated with Cr1R, Major Gene for Resistance to White Pine Blister Rust in Range-Wide Samples of Sugar Pine (Pinus lambertiana).

Sugar pine, Pinus lambertiana Douglas, is a keystone species of montane forests from Baja California to southern Oregon. Like other North American white pines, populations of sugar pine have been greatly reduced by the disease white pine blister rust (WPBR) caused by a fungal pathogen, Cronartium ribicola, that was introduced into North America early in the twentieth century. Major gene resistance to WPBR segregating in natural populations has been documented in sugar pine. Indeed, the dominant resistance gene in this species, Cr1, was genetically mapped, although not precisely. Genomic single nucleotide polymorphisms (SNPs) placed in a large scaffold were reported to be associated with the allele for this major gene resistance (Cr1R). Forest restoration efforts often include sugar pine seed derived from the rare resistant individuals (typically Cr1R/Cr1r) identified through an expensive 2-year phenotypic testing program. To validate and geographically characterize the variation in this association and investigate its potential to expedite genetic improvement in forest restoration, we developed a simple PCR-based, diploid genotyping of DNA from needle tissue. By applying this to range-wide samples of susceptible and resistant (Cr1R) trees, we show that the SNPs exhibit a strong, though not complete, association with Cr1R. Paralleling earlier studies of the geographic distribution of Cr1R and the inferred demographic history of sugar pine, the resistance-associated SNPs are marginally more common in southern populations, as is the frequency of Cr1R. Although the strength of the association of the SNPs with Cr1R and thus, their predictive value, also varies with geography, the potential value of this new tool in quickly and efficiently identifying candidate WPBR-resistant seed trees is clear.

Applying landscape genomic tools to forest management and restoration of Hawaiian koa (Acacia koa) in a changing environment.

Identifying and quantifying the importance of environmental variables in structuring population genetic variation can help inform management decisions for conservation, restoration, or reforestation purposes, in both current and future environmental conditions. Landscape genomics offers a powerful approach for understanding the environmental factors that currently associate with genetic variation, and given those associations, where populations may be most vulnerable under future environmental change. Here, we applied genotyping by sequencing to generate over 11,000 single nucleotide polymorphisms from 311 trees and then used nonlinear, multivariate environmental association methods to examine spatial genetic structure and its association with environmental variation in an ecologically and economically important tree species endemic to Hawaii, Acacia koa. Admixture and principal components analyses showed that trees from different islands are genetically distinct in general, with the exception of some genotypes that match other islands, likely as the result of recent translocations. Gradient forest and generalized dissimilarity models both revealed a strong association between genetic structure and mean annual rainfall. Utilizing a model for projected future climate on the island of Hawaii, we show that predicted changes in rainfall patterns may result in genetic offset, such that trees no longer may be genetically matched to their environment. These findings indicate that knowledge of current and future rainfall gradients can provide valuable information for the conservation of existing populations and also help refine seed transfer guidelines for reforestation or replanting of koa throughout the state.

Genetic conservation and management of the California endemic, Torrey pine (Pinus torreyana Parry): Implications of genetic rescue in a genetically depauperate species.

Rare species present a challenge under changing environmental conditions as the genetic consequences of rarity may limit species ability to adapt to environmental change. To evaluate the evolutionary potential of a rare species, we assessed variation in traits important to plant fitness using multigenerational common garden experiments. Torrey pine, Pinus torreyana Parry, is one of the rarest pines in the world, restricted to one mainland and one island population. Morphological differentiation between island and mainland populations suggests adaptation to local environments may have contributed to trait variation. The distribution of phenotypic variances within the common garden suggests distinct population-specific growth trajectories underlay genetic differences, with the island population exhibiting substantially reduced genetic variance for growth relative to the mainland population. Furthermore, F1 hybrids, representing a cross between mainland and island trees, exhibit increased height accumulation and fecundity relative to mainland and island parents. This may indicate genetic rescue via intraspecific hybridization could provide the necessary genetic variation to persist in environments modified as a result of climate change. Long-term common garden experiments, such as these, provide invaluable resources to assess the distribution of genetic variance that may inform conservation strategies to preserve evolutionary potential of rare species, including genetic rescue.

Genic diversity, genetic structure, and mating system of Brewer spruce (Pinaceae), a relict of the Arcto-Tertiary forest.

Brewer spruce (Picea breweriana), a relict of the widespread Arcto-Tertiary forests, is now restricted to a highly fragmented range in the Klamath Region of California and Oregon. Expected heterozygosity for 26 isozyme loci, averaged over 10 populations, was 0.121. More notable than the relatively high level of diversity when compared to other woody endemics was the strong decrease in expected heterozygosity with latitude. Differentiation (F(ST)) was 0.152, higher than values for many north temperate conifers with larger distributions. The number of migrants per generation (Nm) was 1.34 or 2.70, depending on the method of estimation. Inbreeding appeared low; F(IS) was only 0.003, in agreement with multilocus population outcrossing rates (t(m)), which were generally well above 0.90. No difference in t(m) was found between isolated vs. clustered trees. However, the number of seeds per cone was greatest in the densest populations; t(m) is a measure of effective outcrossing after mortality in the embryonic stage, whereas a reduced number of seeds per cone indicates self pollination. Selfing increased after logging; outcrossing rate before logging was 0.961 and after logging, 0.756. Despite Brewer spruce's narrow, fragmented distribution, the outlook for its conservation was good, with the exception of possible negative effects of logging.

EVIDENCE FOR AN EXTREME BOTTLENECK IN A RARE MEXICAN PINYON: GENETIC DIVERSITY, DISEQUILIBRIUM, AND THE MATING SYSTEM IN PINUS MAXIMARTINEZII.

Maxipiñon (Pinus maximartinezii Rzedowski), which is confined to a single population of approximately 2000 to 2500 mature trees, covers about 400 ha in southern Zacatecas, Mexico. Genetic diversity measured by expected heterozygosity was 0.122, which is moderate for pines. However, percentage polymorphic loci was low, 30.3%. The fixation index (F) of 0.081 indicated only slight heterozygote deficiency. Mating system analysis indicated a significant but low level of selling; the multilocus outcrossing rate, tm , was 0.816. The mean of single locus estimates, ts , was smaller (0.761), perhaps suggesting mating among relatives, although the difference between tm and ts was not statistically significant. The most striking features of maxipiñon's genetic structure were that no polymorphic locus had more than two alleles and most alleles at polymorphic loci were at intermediate frequencies. This is in contrast to other pines, which often have three to five or more alleles at some loci and in which the distribution of allele frequencies is U-shaped, most alleles being present at frequencies less than 10% or greater than 90%. A population with only two alleles per locus and at intermediate frequencies could occur if the population had been reduced to an extreme bottleneck and then expanded rapidly before random drift modified allele frequencies. A novel origin from a hybridization event would also explain the results. Significant gametic disequilibrium was detected at several pairs of loci in both maternal and paternal gametes. The presence of disequilibrium is in agreement with an origin from an extreme bottleneck, perhaps even a single seed. Furthermore, it demands that the event be relatively recent. The number of generations, as calculated from the observed mean disequilibrium, suggested that maxipiñon derived from an extreme bottleneck four to five generations ago, which is less than 1000 years in this species.

RECENT EVOLUTION AND DIVERGENCE AMONG POPULATIONS OF A RARE MEXICAN ENDEMIC, CHIHUAHUA SPRUCE, FOLLOWING HOLOCENE CLIMATIC WARMING.

Fragmentation and reduction in population size are expected to reduce genetic diversity. However, examples from natural populations of forest trees are scarce. The range of Chihuahua spruce retreated northward and fragmented coincident with the warming climate that marked the early Holocene. The isolated populations vary from 15 to 2441 trees, which provided an opportunity to test whether census number is a good predictor of genetic diversity. Mean expected heterozygosity, He , based on 24 loci in 16 enzyme systems, was 0.093 for 10 sampled populations, which is within the range reported for conifers. However, estimates varied more than twofold among populations and He was closely related to the logarithm of the number of mature trees in the population (rHe,N = 0.93). Diversity among populations, FST , was 24.8% of the total diversity, which is higher than that observed in almost all conifer species studied. Nei's genetic distance, D, was not related to geographic distance between populations, and D̄ was 0.033, which is higher than estimates for most wide-ranging species. Most populations had excess homozygosity and the fixation index, FIS , was higher than that reported for all but one species of conifer. Nm, the number of migrants per generation, was 0.43 to 0.76, depending on estimation procedure, and is the smallest observed in conifers. The data suggest that populations of Chihuahua spruce have differentiated by drift and that they are effectively isolated. The results illustrate how a combination of paleontological observation and molecular markers can be used to illuminate recent evolutionary events. Multilocus estimates of outcrossing for two small populations were zero (complete selfing) and 0.153, respectively, which are in striking contrast to the near complete outcrossing observed in most conifers. The high fixation index and a high proportion of empty seeds (45%) suggest that inbreeding may be a serious problem for conservation of Chihuahua spruce.